sybil: printMetabolite-methods – R documentation

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sybil

printMetabolite-methods

Print Rows of the Stoichiometric Matrix

Description

Print the rows of the stoichiometric matrix or an FBA model in CPLEX LP file format.

Usage

## S4 method for signature 'modelorg'
printMetabolite(object, met, FBAlp = FALSE, printOut = TRUE, ...)

Arguments

`object`	An object of class `modelorg`.
`met`	A numeric or character vector containing the metabolite id's of metabolites to print out. If missing, all metabolites given in the model are used.
`FBAlp`	A single logical value. If set to `TRUE`, the output will be in CPLEX LP file format, including the objective function given in the model and reaction bounds. Additionally, if set to `TRUE`, argument `met` will be ignored; all metabolites present in the model are used. See also Details. Default: `FALSE`.
`printOut`	A single Boolean value. If set to `TRUE`, the desired reactions will be printed via the `cat` function. Default: `TRUE`.
`...`	Further arguments passed to `cat`, e.g. argument `file`.

Details

Metabolite id's beginning with a digit or period will be prefixed by the letter "r", reaction id's beginning with a digit or period will be prefixed by the letter "x" and square brackets in reaction or metabolite id's will be replaced by round brackets.

Value

The modelorg method returns a character vector of length equal to the number of metabolites given in argument met, invisibly. Each string represents the reaction participation of one particular metabolite.

Methods

signature(object = "modelorg"): method to use with objects of class modelorg.

Author(s)

Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>

Maintainer: Mayo Roettger <mayo.roettger@hhu.de>